RetrogeneDB ID: retro_mmur_255

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_1996:21759..22412(-)
• Located in intron of: ENSMICG00000009501

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TIPIN
• Ensembl ID: ENSMICG00000004386
• Aliases: None
• Description: TIMELESS interacting protein [Source:HGNC Symbol;Acc:30750]

Sequence

>retro_mmur_255
ATGCTGGAACCACAGGAGAACGGCATGATGACCCAGCAGACTGTGTGCATGGAGAAGAAACTGTCCTCCTTTCCCACCTC
TAGCCTCTCTGCGACACAGGAGGAGAAGGAGCTGGGCCCACTGAAGGCTGTGGAGTAGCTGCAGCTGCTCCTGCGCCTCC
AGACAACAGTAAGAGGAATGCACCCACGCTGGGTCGTGAGACTGATGCAGAGAGGGGCTTGCAGCCTTAAGGAGTTTGTT
TGACAAGGCAAACTTCAAAGGTAAAGGTCATGAGGCTGAAGACTTGAAGATGCTAATCAGACACAGGGAGCACTGGGCAC
ATAGGCTGTTTCCTAAATCCCAATTTGAGGATTTTATTGACAGAATTGAATACCTGGGAAATAAAAAGGAAGTTTGGAAC
TCTTCAAAACAAATGCGACTTGATCTTGCTATTTTACATGAAAATTTTGTTAGCAGTGATAATGACAGAGGGGAAATGAC
AGCCATGAAGTAAGAGCTACTGAATAGATCCCTTTCTGACAAACTCATCTGAAAGTGAGAAGTTTTCTTCTGAGTCAAGT
AGAAGCCTAACAGAAGAGCCACAACAAAGAATTGAGAGAAATAAACAACTCACCTTGGAAAGAAGGCAGGTAAAGCTCCT
GAGTAAGAGTCAG

Alignment

ORF - retro_mmur_255 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.25 %
• Parental protein coverage: 74.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MLEPQENGMI-DLPDYEHTEDETF-PPFPPPASPERQ-DGEGAEPDEVSGNGAPVPVPPKRTVKRNIPKL
          MLEPQENGM..D..D..H.E.ET..PPF.PP....R...GEGA.P.E..G..A..P.PP....KRN.P.L
Retrocopy MLEPQENGMM<DPADCVHGE-ETV<PPF-PPLASLRH>GGEGAGPTEGCGVAAAAPAPPDNS-KRNAPTL

Parental  DAQRLISERGLP-ALRNLFDKAKFKGKGHEAEDLKTLIRHMEHWAHRLFPKLQFEDFIDRIEYLGNKKEV
          .......ERGL..ALR.LFDKA.FKGKGHEAEDLK.LIRH.EHWAHRLFPK.QFEDFIDRIEYLGNKKEV
Retrocopy -GRETDAERGLQ<ALRSLFDKANFKGKGHEAEDLKMLIRHREHWAHRLFPKSQFEDFIDRIEYLGNKKEV

Parental  QTCLKRIRLDLPIVHEDFVSNDDDIGE-NNSHDITTTE-LDPFLTNSSENEKFAFESSRNLTEEQQQRIE
          ....K..RLDL.I.HE.FVS.D.D.GE.N.SH....TE..DPFLTNSSE.EKF..ESSR.LTEE.QQRIE
Retrocopy WNSSKQMRLDLAILHENFVSSDNDRGE<NDSHEVRATE<IDPFLTNSSESEKFSSESSRSLTEEPQQRIE

Parental  RNKQLALERRQAKLLSNSQ
          RNKQL.LERRQ.KLLS.SQ
Retrocopy RNKQLTLERRQVKLLSKSQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Microcebus murinus was not studied using RNA-Seq expression data.

ChIP-Seq

Microcebus murinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmur_255 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_255 was not experimentally validated.

Homology

Retrocopy orthology:

Microcebus murinus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004860	1 retrocopy	retro_chof_223,
Dasypus novemcinctus	ENSDNOG00000003177	3 retrocopies	retro_dnov_1334, retro_dnov_1481, retro_dnov_410,
Homo sapiens	ENSG00000075131	1 retrocopy	retro_hsap_4837,
Gorilla gorilla	ENSGGOG00000000061	3 retrocopies	retro_ggor_1268, retro_ggor_2907, retro_ggor_3016,
Loxodonta africana	ENSLAFG00000026016	1 retrocopy	retro_lafr_1104,
Microcebus murinus	ENSMICG00000004386	2 retrocopies	retro_mmur_155, retro_mmur_255 ,
Macaca mulatta	ENSMMUG00000003695	1 retrocopy	retro_mmul_1582,
Nomascus leucogenys	ENSNLEG00000012909	1 retrocopy	retro_nleu_1336,
Pan troglodytes	ENSPTRG00000007192	2 retrocopies	retro_ptro_1145, retro_ptro_3220,
Rattus norvegicus	ENSRNOG00000043068	1 retrocopy	retro_rnor_364,